6QSQ

X-ray crystal structure of the R336L Vibrio alkaline phosphatase variant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop.

Hjorleifsson, J.G.Helland, R.Magnusdottir, M.Asgeirsson, B.

(2020) FEBS Open Bio 

  • DOI: https://doi.org/10.1002/2211-5463.13041
  • Primary Citation of Related Structures:  
    6QSQ

  • PubMed Abstract: 

    The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold-adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B-factors of the R336L crystal structure to that of the wild-type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half-of-sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).


  • Organizational Affiliation

    Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline phosphatase512Vibrio splendidusMutation(s): 1 
Gene Names: BCT36_11160
UniProt
Find proteins for A0A2N7KUA1 (Vibrio splendidus)
Explore A0A2N7KUA1 
Go to UniProtKB:  A0A2N7KUA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2N7KUA1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.082α = 90
b = 118.596β = 90
c = 83.922γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIceland141619-051
Research Council of NorwayNorway247732

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description